{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,30]],"date-time":"2024-05-30T08:28:42Z","timestamp":1717057722889},"reference-count":30,"publisher":"Springer Science and Business Media LLC","issue":"S6","license":[{"start":{"date-parts":[[2013,4,1]],"date-time":"2013-04-01T00:00:00Z","timestamp":1364774400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,4]]},"DOI":"10.1186\/1471-2105-14-s6-s5","type":"journal-article","created":{"date-parts":[[2013,4,17]],"date-time":"2013-04-17T11:35:21Z","timestamp":1366198521000},"source":"Crossref","is-referenced-by-count":2,"title":["Software tool for 3D extraction of germinal centers"],"prefix":"10.1186","volume":"14","author":[{"given":"David N","family":"Olivieri","sequence":"first","affiliation":[]},{"given":"Merly","family":"Escalona","sequence":"additional","affiliation":[]},{"given":"Jose","family":"Faro","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,4,17]]},"reference":[{"key":"5803_CR1","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1021\/bi00895a027","volume":"3","author":"HN Eisen","year":"1964","unstructured":"Eisen HN, Siskind GW: Variations in Affinities of Antibodies during the Immune Response. Biochemistry. 1964, 3: 996-1008. 10.1021\/bi00895a027.","journal-title":"Biochemistry"},{"key":"5803_CR2","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1146\/annurev.iy.12.040194.001001","volume":"12","author":"IC MacLennan","year":"1994","unstructured":"MacLennan IC: Germinal centers. Annu Rev Immunol. 1994, 12: 117-139. 10.1146\/annurev.iy.12.040194.001001.","journal-title":"Annu Rev Immunol"},{"issue":"3","key":"5803_CR3","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1006\/smim.1996.0022","volume":"8","author":"G Kelsoe","year":"1996","unstructured":"Kelsoe G: The germinal center: a crucible for lymphocyte selection. Semin Immunol. 1996, 8 (3): 179-184. 10.1006\/smim.1996.0022.","journal-title":"Semin Immunol"},{"issue":"2","key":"5803_CR4","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1016\/j.immuni.2007.07.009","volume":"27","author":"CD Allen","year":"2007","unstructured":"Allen CD, Okada T, Cyster JG: Germinal-center organization and cellular dynamics. Immunity. 2007, 27 (2): 190-202. 10.1016\/j.immuni.2007.07.009.","journal-title":"Immunity"},{"issue":"12","key":"5803_CR5","doi-asserted-by":"publisher","first-page":"6185","DOI":"10.4049\/jimmunol.1101440","volume":"187","author":"N Wittenbrink","year":"2011","unstructured":"Wittenbrink N, Klein A, Weiser AA, Schuchhardt J, Or-Guil M: Is There a Typical Germinal Center? A Large-Scale Immunohistological Study on the Cellular Composition of Germinal Centers during the Hapten-Carrier-Driven Primary Immune Response in Mice. J Immunol. 2011, 187 (12): 6185-6196. 10.4049\/jimmunol.1101440.","journal-title":"J Immunol"},{"key":"5803_CR6","doi-asserted-by":"publisher","first-page":"3369","DOI":"10.4049\/jimmunol.172.6.3369","volume":"172","author":"T Manser","year":"2004","unstructured":"Manser T: Textbook germinal centers?. J Immunol. 2004, 172: 3369-3375.","journal-title":"J Immunol"},{"issue":"9","key":"5803_CR7","doi-asserted-by":"publisher","first-page":"4553","DOI":"10.4049\/jimmunol.1101328","volume":"187","author":"I Wollenberg","year":"2011","unstructured":"Wollenberg I, Agua-Doce A, Hernandez A, Almeida C, Oliveira VG, Faro J, Graca L: Regulation of the germinal center reaction by Foxp3+ follicular regulatory T cells. J Immunol. 2011, 187 (9): 4553-60. 10.4049\/jimmunol.1101328.","journal-title":"J Immunol"},{"issue":"8","key":"5803_CR8","doi-asserted-by":"publisher","first-page":"983","DOI":"10.1038\/nm.2426","volume":"17","author":"Y Chung","year":"2011","unstructured":"Chung Y, Tanaka S, Chu F, Nurieva RI, Martinez GJ, Rawal S, Wang YH, Lim H, Reynolds JM, Zhou XH, Fan HM, Liu ZM, Neelapu SS, Dong C: Follicular regulatory T cells expressing Foxp3 and Bcl-6 suppress germinal center reactions. Nat Med. 2011, 17 (8): 983-8. 10.1038\/nm.2426. [Doi: 10.1038\/nm.2426.]","journal-title":"Nat Med"},{"issue":"8","key":"5803_CR9","doi-asserted-by":"publisher","first-page":"975","DOI":"10.1038\/nm.2425","volume":"17","author":"MA Linterman","year":"2011","unstructured":"Linterman MA, Pierson W, Lee SK, Kallies A, Kawamoto S, Rayner TF, Srivastava M, Divekar DP, Beaton L, Hogan JJ, Fagarasan S, Liston A, Smith KG, Vinuesa CG: Foxp3+ follicular regulatory T cells control the germinal center response. Nat Med. 2011, 17 (8): 975-82. 10.1038\/nm.2425. [Doi: 10.1038\/nm.2425.]","journal-title":"Nat Med"},{"issue":"12","key":"5803_CR10","doi-asserted-by":"publisher","first-page":"i57","DOI":"10.1093\/bioinformatics\/btq219","volume":"26","author":"S Saalfeld","year":"2010","unstructured":"Saalfeld S, Cardona A, Hartenstein V, Tomancak P: As rigid as possible mosaicking and serial section registration of larte ssTEM datasets. Bioinformatics. 2010, 26 (12): i57-i63. 10.1093\/bioinformatics\/btq219.","journal-title":"Bioinformatics"},{"issue":"10","key":"5803_CR11","doi-asserted-by":"publisher","first-page":"e1000502","DOI":"10.1371\/journal.pbio.1000502","volume":"8","author":"A Cardona","year":"2010","unstructured":"Cardona A, Saalfeld S, Preibisch S, Schmid B, Cheng A, Pulokas J, Tomancak P, Hartenstein V: An integrated micro- and Macroarchitectural Analysis of the Drosophila Brain by computer-Assisted serial section Electron Microscopy. PLoS Biol. 2010, 8 (10): e1000502-10.1371\/journal.pbio.1000502.","journal-title":"PLoS Biol"},{"key":"5803_CR12","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/S0262-8856(00)00052-4","volume":"19","author":"S Ourselin","year":"2001","unstructured":"Ourselin S, Roche A, Subsol G, Pnnec X, Ayache N: Reconstructing a 3d structure from serial histological sections. Image and Vision Computing. 2001, 19: 25-31. 10.1016\/S0262-8856(00)00052-4.","journal-title":"Image and Vision Computing"},{"issue":"3 Suppl","key":"5803_CR13","doi-asserted-by":"publisher","first-page":"S26","DOI":"10.1038\/nmeth.1431","volume":"7","author":"T Walter","year":"2010","unstructured":"Walter T, Shattuck DW, Baldock R, Bastin ME, Carpenter AE, Duce S, Ellenberg J, Fraser A, Hamilton N, Pieper S, Ragan MA, Schneider JE, Tomancak P, Heriche JK: Visualization of image data from cells to organisms. Nat Methods. 2010, 7 (3 Suppl): S26-S41.","journal-title":"Nat Methods"},{"key":"5803_CR14","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1146\/annurev.biophys.050708.133641","volume":"38","author":"J Swedlow","year":"2009","unstructured":"Swedlow J, Goldberg I, Eliceiri K, the OME Consortium: Bioimage Informatics for Experimental Biology. Annu Rev Biophys. 2009, 38: 327-346. 10.1146\/annurev.biophys.050708.133641.","journal-title":"Annu Rev Biophys"},{"issue":"11","key":"5803_CR15","doi-asserted-by":"publisher","first-page":"1463","DOI":"10.1093\/bioinformatics\/btp184","volume":"25","author":"S Preibisch","year":"2009","unstructured":"Preibisch S, Saalfeld S, Tomancak P: Globally optimal stitching of tiled 3D microscopic image acquisitions. Bioinformatics. 2009, 25 (11): 1463-1465. 10.1093\/bioinformatics\/btp184.","journal-title":"Bioinformatics"},{"key":"5803_CR16","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1007\/11889762_8","volume":"4241","author":"I I Arganda-Carreras","year":"2006","unstructured":"I Arganda-Carreras I, Sorzano C, Marabini R, Carazo J, Ortiz de Solorzano C, Kybic J: Consistent and Elastic Registration of Histologic sections using vector spline regularization. Lecture Notes in Computer Science, Springer, CVAMIA. 2006, 4241: 85-95. 10.1007\/11889762_8.","journal-title":"Lecture Notes in Computer Science, Springer, CVAMIA"},{"issue":"11","key":"5803_CR17","doi-asserted-by":"publisher","first-page":"977","DOI":"10.1016\/S0262-8856(03)00137-9","volume":"21","author":"B Zitov\u00e1","year":"2003","unstructured":"Zitov\u00e1 B, Flusser J: Image registration methods: a survey. Image and Vision Computing. 2003, 21 (11): 977-1000. 10.1016\/S0262-8856(03)00137-9. [\n                    http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0262885603001379\n                    \n                  ]","journal-title":"Image and Vision Computing"},{"key":"5803_CR18","first-page":"69142V","volume-title":"Proceedings of SPIE, Volume 6914","author":"U Bagci","year":"2009","unstructured":"Bagci U, Bai L: Registration of standardized histological images in feature space. Proceedings of SPIE, Volume 6914. 2009, Spie, 69142V-69142V-9. [\n                    http:\/\/arxiv.org\/abs\/0907.3209\n                    \n                  ]"},{"issue":"2","key":"5803_CR19","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1016\/S1361-8415(96)80007-7","volume":"1","author":"I McInerney","year":"1996","unstructured":"McInerney I, Terzopoulus T: Deformable Model sin Medical Image Analysis: A Survey. Medical Image Analysis. 1996, 1 (2): 91-108. 10.1016\/S1361-8415(96)80007-7.","journal-title":"Medical Image Analysis"},{"issue":"2","key":"5803_CR20","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1111\/j.1365-2818.2011.03486.x","volume":"243","author":"M Laasmaa","year":"2011","unstructured":"Laasmaa M, Vendelin M, Peterson P: Application of regularized Richardson-Lucy algorithm for deconvolution of confocal microscopy images. J Microsc. 2011, 243 (2): 124-140. 10.1111\/j.1365-2818.2011.03486.x.","journal-title":"J Microsc"},{"issue":"3","key":"5803_CR21","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1017\/S1551929500057606","volume":"14","author":"P Kankaanp\u00e4\u00e4","year":"2006","unstructured":"Kankaanp\u00e4\u00e4 P, Pahajoki K, Marjom\u00e4ki V, Heino J, White D: BioImageXD - New Open Source Free Software for the Processing, Analysis and Visualization of Multidimensional Microscopic Images. Microscopy Today. 2006, 14 (3): 12-16.","journal-title":"Microscopy Today"},{"key":"5803_CR22","doi-asserted-by":"publisher","first-page":"199","DOI":"10.2144\/000112224","volume":"41","author":"D Schiffmann","year":"2006","unstructured":"Schiffmann D, Dikovskaya D, Appleton P, Newton I, Creager D, Allan C, Nathke I, Goldberg I: Open Microscopy Environment and FindSpots: integrating image informatics with quantitative multidimensional image analysis. BioTechniques. 2006, 41: 199-207. 10.2144\/000112224.","journal-title":"BioTechniques"},{"issue":"2-3","key":"5803_CR23","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1016\/S0925-7721(01)00017-7","volume":"19","author":"N Amenta","year":"2001","unstructured":"Amenta N, Choi S, Kolluri R: The power crust, unions of balls, and the medial axis transform. Computational Geometry: Theory and Applications. 2001, 19 (2-3): 127-153. 10.1016\/S0925-7721(01)00017-7.","journal-title":"Computational Geometry: Theory and Applications"},{"issue":"5","key":"5803_CR24","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1083\/jcb.201004104","volume":"189","author":"M Linkertm","year":"2010","unstructured":"Linkertm M, Rueden C, Allan C, Burel J, Moore W, Patterson A, Loranger B, Moore J, Neves C, Macdonald D, Tarkowska A, Sticco C, Hill E, Rossner M, Eliceiri K, Swedlow J: Metadata matters: access to image data in the real world. J Cell Biol. 2010, 189 (5): 777-782. 10.1083\/jcb.201004104.","journal-title":"J Cell Biol"},{"key":"5803_CR25","volume-title":"Computer vision","author":"LG Shapiro","year":"2001","unstructured":"Shapiro LG, Stockman GC: Computer vision. 2001, Upper Saddle River, NJ: Prentice Hall"},{"key":"5803_CR26","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-84882-935-0","volume-title":"Computer Vision: Algorithms and Applications","author":"R Szeliski","year":"2011","unstructured":"Szeliski R: Computer Vision: Algorithms and Applications. 2011, Berlin, Germany: Springer"},{"issue":"3","key":"5803_CR27","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1109\/TMI.2011.2180920","volume":"31","author":"U Bagci","year":"2012","unstructured":"Bagci U, Chen X, Udupa J: Hierarchical Scale-Based Multiobject Recognition of 3-D Anatomical Structures. IEEE Trans Med Imaging. 2012, 31 (3): 777-789.","journal-title":"IEEE Trans Med Imaging"},{"key":"5803_CR28","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1006\/gmip.1998.0465","volume":"60","author":"N Amenta","year":"1998","unstructured":"Amenta N, Bern M, Eppstein D: The Crust and the Beta-Skeleton: Combinatorial Curve Reconstruction. Graphical Models and Image Processing. 1998, 60: 125-135. 10.1006\/gmip.1998.0465.","journal-title":"Graphical Models and Image Processing"},{"key":"5803_CR29","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1145\/376957.376986","volume-title":"Proceedings of the sixth ACM symposium on Solid modeling and applications","author":"N Amenta","year":"2001","unstructured":"Amenta N, Choi S, Kolluri R: The power crust. Proceedings of the sixth ACM symposium on Solid modeling and applications. 2001, SMA '01, New York, NY, USA: ACM, 249-266. [\n                    http:\/\/doi.acm.org\/10.1145\/376957.376986\n                    \n                  ]"},{"key":"5803_CR30","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1007\/PL00009475","volume":"22","author":"N Amenta","year":"1999","unstructured":"Amenta N, Bern M: Surface Reconstruction by Voronoi Filtering. Discrete and Computational Geometry. 1999, 22: 481-504. 10.1007\/PL00009475.","journal-title":"Discrete and Computational Geometry"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S6-S5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-14-S6-S5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S6-S5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T11:11:58Z","timestamp":1548155518000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-S6-S5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,4]]},"references-count":30,"journal-issue":{"issue":"S6","published-print":{"date-parts":[[2013,4]]}},"alternative-id":["5803"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-s6-s5","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,4]]},"article-number":"S5"}}